March 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] ff5c6f: fix target for 101 rewrite
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ff5c6fe5bb2b146736696597fa7927b901be7528 https://github.com/galaxyproject/usegalaxy-playbook/commit/ff5c6fe5bb2b1467… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M templates/nginx/usegalaxy_rewrites.conf.j2 Log Message: ----------- fix target for 101 rewrite the canonical source is in the hub

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[galaxyproject/infrastructure-playbook] c1e905: Remove extra Jetstream instances
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c1e90571202d3d1ca9a3d0242ecc27595ad2e168 https://github.com/galaxyproject/infrastructure-playbook/commit/c1e90571202… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M jetstreamiuenv/inventory M jetstreamtaccenv/inventory Log Message: ----------- Remove extra Jetstream instances

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[galaxyproject/galaxy] 12eb38: fix xss thanks to @erasche
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 12eb3838496f373e429235cd8e75117baf682005 https://github.com/galaxyproject/galaxy/commit/12eb3838496f373e429235cd8e75… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- fix xss thanks to @erasche Commit: 2528a89bd087786c458c86d6ac78c24e8fb7f51d https://github.com/galaxyproject/galaxy/commit/2528a89bd087786c458c86d6ac78… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3776 from martenson/xss-fix [16.04] fix xss vuln in grids Compare: https://github.com/galaxyproject/galaxy/compare/4cf70aea7977...2528a89bd087

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[galaxyproject/galaxy] 131aeb: Abstract uWSGI handling into new galaxy.web.stack ...
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 131aeb66b4884200c6c9433aef9a80aabf98d132 https://github.com/galaxyproject/galaxy/commit/131aeb66b4884200c6c9433aef9a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/watcher.py R lib/galaxy/util/postfork.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/sentry.py A lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/util.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Abstract uWSGI handling into new galaxy.web.stack package. Commit: d18b4d13cbc25c85005e4b19a02abedbed7aba46 https://github.com/galaxyproject/galaxy/commit/d18b4d13cbc25c85005e4b19a02a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/util.py Log Message: ----------- Add an exception for unsupported middleware wrapping for better failure handling. Commit: 5440889bf6a7c5f278860760cd8c4ba18708c263 https://github.com/galaxyproject/galaxy/commit/5440889bf6a7c5f278860760cd8c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/watcher.py R lib/galaxy/util/postfork.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/sentry.py A lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/util.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Merge pull request #3759 from natefoo/abstract-app-stack Abstract uWSGI handling into new galaxy.web.stack package Compare: https://github.com/galaxyproject/galaxy/compare/cd36aa0878ae...5440889bf6a7

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[galaxyproject/infrastructure-playbook] 1426a8: Update athena access list
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1426a8538568204c47adc82a92ddef6953b77eb4 https://github.com/galaxyproject/infrastructure-playbook/commit/1426a853856… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M galaxyenv/secret_host_vars/athena.galaxyproject.org.yml Log Message: ----------- Update athena access list

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[galaxyproject/infrastructure-playbook] c42389: add hub redirects for API pages
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c42389db42d441f7ba3828e8fcf39dfaff0fef88 https://github.com/galaxyproject/infrastructure-playbook/commit/c42389db42d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M galaxyenv/templates/nginx/galaxyproject.j2 Log Message: ----------- add hub redirects for API pages

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[galaxyproject/galaxy] 376212: Fix for uploading rdata datasets when explicitly d...
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: 376212eff900d28450165ddf715f3d9a29870ca9 https://github.com/galaxyproject/galaxy/commit/376212eff900d28450165ddf715f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix for uploading rdata datasets when explicitly declaring datatype. Now that ext's are forced to be all lowercase, you cannot upload a dataset with any uppercase characters in the extension. TODO: An additional fix directly for the upload tool/datatype widget should be pursued that will prevent these issues. Commit: e3e24facc72103dadeca2dc72c9d038f907eb10e https://github.com/galaxyproject/galaxy/commit/e3e24facc72103dadeca2dc72c9d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #3766 from blankenberg/17.01-rdata-upload-fix [17.01] Fix for uploading rdata datasets when explicitly declaring datatype. Commit: 3b4cf0d578d871f8bf3e005e0b5d7c65c78d1b2d https://github.com/galaxyproject/galaxy/commit/3b4cf0d578d871f8bf3e005e0b5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #3778 from galaxyproject/release_17.01 [usegalaxy] merge Release 17.01 Compare: https://github.com/galaxyproject/galaxy/compare/f76e0921d7d2...3b4cf0d578d8

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[galaxyproject/usegalaxy-playbook] d37d80: Add Dockerfiles for galaxy-update and galaxy-insta...
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d37d808bf7a6f3b8e5688fd0581289deb0aca4ab https://github.com/galaxyproject/usegalaxy-playbook/commit/d37d808bf7a6f3b8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: A common/docker/galaxy-installer/Dockerfile.main A common/docker/galaxy-installer/Dockerfile.test A common/docker/galaxy-installer/run_main.sh A common/docker/galaxy-installer/run_test.sh A common/docker/galaxy-update/Dockerfile A common/docker/galaxy-update/condarc Log Message: ----------- Add Dockerfiles for galaxy-update and galaxy-installer. Note galaxy.ini not included.

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[galaxyproject/galaxy] 77b298: Fix run_tests.sh --dockerize for Mac OS X usage.
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 77b29880c8e9eddaf282e8738542aa57a189f6d2 https://github.com/galaxyproject/galaxy/commit/77b29880c8e9eddaf282e8738542… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M run_tests.sh Log Message: ----------- Fix run_tests.sh --dockerize for Mac OS X usage. Without this I get the error message below and the tests do not execute. ``` ./run_tests.sh: line 279: UID: readonly variable ``` This was likely broken with b75ee68d9f6305646a55d816fb1173210e36eab9. Commit: d1eab2685f652f0b6f8c8119c51acf080c54556e https://github.com/galaxyproject/galaxy/commit/d1eab2685f652f0b6f8c8119c51a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Provide a fallback for GALAXY_TEST_UID if manually running Docker tests. Commit: d6654838f361a1e3064619cb059f9137579dc376 https://github.com/galaxyproject/galaxy/commit/d6654838f361a1e3064619cb059f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Fix pip install cache inside Galaxy testing container. It is causing Jenkins to fail throughout on https://github.com/galaxyproject/galaxy/pull/3179. Commit: b1f12d41f66c2b07929c037363fc6d94b890b283 https://github.com/galaxyproject/galaxy/commit/b1f12d41f66c2b07929c037363fc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Simplify run_test_wrapper.sh per @natefoo comments. https://github.com/galaxyproject/galaxy/pull/3755/files#r106182107 Commit: cd36aa0878aed1a604a256098241068df169e4a3 https://github.com/galaxyproject/galaxy/commit/cd36aa0878aed1a604a256098241… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M run_tests.sh M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #3755 from jmchilton/docker_test_fixes Assorted Fixes for Dockerized Test Setup Compare: https://github.com/galaxyproject/galaxy/compare/8e77fe93b8e0...cd36aa0878ae

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[galaxyproject/galaxy] 376212: Fix for uploading rdata datasets when explicitly d...
by GitHub 20 Mar '17

20 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 376212eff900d28450165ddf715f3d9a29870ca9 https://github.com/galaxyproject/galaxy/commit/376212eff900d28450165ddf715f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix for uploading rdata datasets when explicitly declaring datatype. Now that ext's are forced to be all lowercase, you cannot upload a dataset with any uppercase characters in the extension. TODO: An additional fix directly for the upload tool/datatype widget should be pursued that will prevent these issues. Commit: e3e24facc72103dadeca2dc72c9d038f907eb10e https://github.com/galaxyproject/galaxy/commit/e3e24facc72103dadeca2dc72c9d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #3766 from blankenberg/17.01-rdata-upload-fix [17.01] Fix for uploading rdata datasets when explicitly declaring datatype. Compare: https://github.com/galaxyproject/galaxy/compare/6ab5cc1caf8c...e3e24facc721

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